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<h1 id="installation-instructions">Installation instructions</h1>
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<h2 id="system-requirements">System requirements</h2>
<p>This package is supported for Linux, but should also work on Mac OS X and Windows. It has been tested with <a href="https://github.com/dynverse/dyngen/actions?query=workflow%3AR-CMD-check">Github Actions</a> for R 3.5, 3.6 and 4.0 on the following systems Ubuntu, Windows Server and Mac OS X.</p>
<h2 id="step-1-installing-from-cran-or-github-required">Step 1: Installing from CRAN or GitHub (Required)</h2>
<p>dyngen is available on CRAN, so you can install it with the following command.</p>
<div class="sourceCode" id="cb1"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb1-1"><a href="#cb1-1" aria-hidden="true" tabindex="-1"></a><span class="fu">install.packages</span>(<span class="st">&quot;dyngen&quot;</span>)</span></code></pre></div>
<p>If you would like to install the development version of dyngen from GitHub instead, run the following command. Use at your own risk!</p>
<div class="sourceCode" id="cb2"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb2-1"><a href="#cb2-1" aria-hidden="true" tabindex="-1"></a><span class="fu">install.packages</span>(<span class="st">&quot;remotes&quot;</span>)</span>
<span id="cb2-2"><a href="#cb2-2" aria-hidden="true" tabindex="-1"></a>remotes<span class="sc">::</span><span class="fu">install_github</span>(<span class="st">&quot;dynverse/dyngen@devel&quot;</span>, <span class="at">dependencies =</span> <span class="cn">TRUE</span>)</span></code></pre></div>
<h2 id="step-2-configure-host-system-recommended">Step 2: Configure host system (Recommended)</h2>
<p>It’s recommended to let dyngen know where it can cache downloaded files and how many cores the host system has. If you don’t perform these steps, running dyngen simulations will take a lot longer than it needs to.</p>
<p>To do so, start editing your Rprofile by running the following commands:</p>
<div class="sourceCode" id="cb3"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb3-1"><a href="#cb3-1" aria-hidden="true" tabindex="-1"></a><span class="fu">install.packages</span>(<span class="st">&quot;usethis&quot;</span>)</span>
<span id="cb3-2"><a href="#cb3-2" aria-hidden="true" tabindex="-1"></a>usethis<span class="sc">::</span><span class="fu">edit_r_profile</span>()</span></code></pre></div>
<p>Inside your Rprofile, add the following lines:</p>
<div class="sourceCode" id="cb4"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb4-1"><a href="#cb4-1" aria-hidden="true" tabindex="-1"></a><span class="fu">options</span>(<span class="at">Ncpus =</span> 8L) <span class="co"># change this to the number of cores in your system</span></span>
<span id="cb4-2"><a href="#cb4-2" aria-hidden="true" tabindex="-1"></a><span class="fu">options</span>(<span class="at">dyngen_download_cache_dir =</span> <span class="fu">R_user_dir</span>(<span class="st">&quot;dyngen&quot;</span>, <span class="st">&quot;data&quot;</span>))</span></code></pre></div>
<p>After saving and closing this file, restart your R sesstion.</p>
<h2 id="step-3-download-cacheable-files-optional">Step 3: Download cacheable files (Optional)</h2>
<p>dyngen will sometimes download files from GitHub and cache them for later use (if you executed step 2). After installation, you can already download these files so they will not be downloaded at a later stage.</p>
<div class="sourceCode" id="cb5"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb5-1"><a href="#cb5-1" aria-hidden="true" tabindex="-1"></a><span class="fu">library</span>(utils)</span>
<span id="cb5-2"><a href="#cb5-2" aria-hidden="true" tabindex="-1"></a><span class="fu">library</span>(tools)</span>
<span id="cb5-3"><a href="#cb5-3" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb5-4"><a href="#cb5-4" aria-hidden="true" tabindex="-1"></a>zip <span class="ot">&lt;-</span> <span class="fu">tempfile</span>(<span class="at">fileext =</span> <span class="st">&quot;.zip&quot;</span>)</span>
<span id="cb5-5"><a href="#cb5-5" aria-hidden="true" tabindex="-1"></a><span class="fu">download.file</span>(<span class="st">&quot;https://github.com/dynverse/dyngen/archive/data_files.zip&quot;</span>, zip)</span>
<span id="cb5-6"><a href="#cb5-6" aria-hidden="true" tabindex="-1"></a><span class="fu">unzip</span>(zip, <span class="at">exdir =</span> <span class="fu">getOption</span>(<span class="st">&quot;dyngen_download_cache_dir&quot;</span>), <span class="at">overwrite =</span> <span class="cn">TRUE</span>)</span></code></pre></div>

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